Tue Oct 7 05:02:31 2014
SigFuge
thresh_junctionfilter_num_present_samples (8)thresh_junctionfilter_present_support (5)coverageThreshold_exon (.5)coverageThreshold_intron (10)## gIdx gStart gStop kind start stop s1 s2 s3 ## 107 gene56 119793 119838 e 119793 119838 0.00 2.283 2.478 ## 108 gene57 119919 119953 e 119919 119953 1.00 3.771 2.743 ## 109 gene58 121312 179059 e 121312 121573 128.51 185.855 117.916 ## 110 gene58 121312 179059 j 121573 121961 95.00 249.000 32.000 ## 111 gene58 121312 179059 j 121573 123217 0.00 5.000 1.000 ## 112 gene58 121312 179059 e 121574 121960 10.32 27.439 8.796 ## 113 gene58 121312 179059 e 121961 122090 314.45 384.592 181.223 ## 114 gene58 121312 179059 j 122090 123217 354.00 335.000 23.000 ## 115 gene58 121312 179059 e 123217 123282 411.89 352.758 127.409 ## 116 gene58 121312 179059 j 123282 123386 301.00 277.000 136.000
compute distribution of average expression over each exon and plot distributions grouped by the number of exons each gene
## [1] TRUE
gene1791 componentlook at clusters
## 15 x 15 sparse Matrix of class "dgCMatrix" ## ## [1,] 75 . 170 . . . . . . . . . . . . ## [2,] . 30 . . . . . . . . . . . . . ## [3,] . . 118 24 . . . . . . . . . . . ## [4,] . . . 24 6 . . 12 . . 3 . . . . ## [5,] . . . . 7 . . . . . . . . . . ## [6,] . . . . . 5 5 . . . . . . . . ## [7,] . . . . . . 12 2 . . 4 . . . . ## [8,] . . . . . . . 16 . . . . . . . ## [9,] . . . . . . . . . . . . . . . ## [10,] . . . . . . . . . 1 1 . . . . ## [11,] . . . . . . . . . . 17 . . 7 . ## [12,] . . . . . . . . . . . 61 37 . . ## [13,] . . . . . . . . . . . . 109 . . ## [14,] . . . . . . . . . . . . . 6 . ## [15,] . . . . . . . . . . . . . . 4
R EnvironmentR EnvironmentRunning time:
proc.time() - start_time ## user system elapsed ## 47.536 1.181 48.936
Compiled on:
Sys.time() ## [1] "2014-10-07 05:03:20 EDT"
R EnvironmentSession Information:
sessionInfo() ## R version 3.1.1 (2014-07-10) ## Platform: x86_64-apple-darwin13.3.0 (64-bit) ## ## locale: ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 ## ## attached base packages: ## [1] grid parallel stats graphics grDevices utils datasets ## [8] methods base ## ## other attached packages: ## [1] rmarkdown_0.3.3 ## [2] mvnmle_0.1-11 ## [3] igraph_0.7.1 ## [4] PTAk_1.2-9 ## [5] tensor_1.5 ## [6] org.Hs.eg.db_2.14.0 ## [7] RSQLite_0.11.4 ## [8] DBI_0.3.1 ## [9] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 ## [10] BSgenome.Hsapiens.UCSC.hg19_1.3.1000 ## [11] annotate_1.42.1 ## [12] SplicingGraphs_1.4.1 ## [13] Rgraphviz_2.8.1 ## [14] graph_1.42.0 ## [15] GenomicAlignments_1.0.6 ## [16] BSgenome_1.32.0 ## [17] Rsamtools_1.16.1 ## [18] Biostrings_2.32.1 ## [19] XVector_0.4.0 ## [20] GenomicFeatures_1.16.3 ## [21] AnnotationDbi_1.26.1 ## [22] Biobase_2.24.0 ## [23] GenomicRanges_1.16.4 ## [24] GenomeInfoDb_1.0.2 ## [25] IRanges_1.22.10 ## [26] RColorBrewer_1.0-5 ## [27] ggbio_1.12.10 ## [28] BiocGenerics_0.10.0 ## [29] ggplot2_1.0.0 ## ## loaded via a namespace (and not attached): ## [1] acepack_1.3-3.3 base64enc_0.1-2 ## [3] BatchJobs_1.4 BBmisc_1.7 ## [5] BiocParallel_0.6.1 biomaRt_2.20.0 ## [7] biovizBase_1.12.3 bitops_1.0-6 ## [9] brew_1.0-6 caTools_1.17.1 ## [11] checkmate_1.4 cluster_1.15.3 ## [13] codetools_0.2-9 colorspace_1.2-4 ## [15] compiler_3.1.1 dichromat_2.0-0 ## [17] digest_0.6.4 evaluate_0.5.5 ## [19] fail_1.2 foreach_1.4.2 ## [21] foreign_0.8-61 formatR_1.0 ## [23] Formula_1.1-2 gridExtra_0.9.1 ## [25] gtable_0.1.2 Hmisc_3.14-5 ## [27] htmltools_0.2.6 iterators_1.0.7 ## [29] knitr_1.6 labeling_0.3 ## [31] lattice_0.20-29 latticeExtra_0.6-26 ## [33] MASS_7.3-35 Matrix_1.1-4 ## [35] munsell_0.4.2 nnet_7.3-8 ## [37] plyr_1.8.1 proto_0.3-10 ## [39] Rcpp_0.11.3 RCurl_1.95-4.3 ## [41] reshape2_1.4 rpart_4.1-8 ## [43] rtracklayer_1.24.2 scales_0.2.4 ## [45] sendmailR_1.2-1 splines_3.1.1 ## [47] stats4_3.1.1 stringr_0.6.2 ## [49] survival_2.37-7 tools_3.1.1 ## [51] VariantAnnotation_1.10.5 XML_3.98-1.1 ## [53] xtable_1.7-4 yaml_2.1.13 ## [55] zlibbioc_1.10.0